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37 results on '"Brukhin, Vladimir"'

1. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Author

Kliver, Sergei, Rayko, Mike, Komissarov, Alexey, Bakin, Evgeny, Zhernakova, Daria, Prasad, Kasavajhala, Rushworth, Catherine, Baskar, R, Smetanin, Dmitry, Schmutz, Jeremy, Rokhsar, Daniel S, Mitchell-Olds, Thomas, Grossniklaus, Ueli, and Brukhin, Vladimir

Subjects
Boechera, Brassicaceae, annotation, apomixis, assembly, genome, Genetics
Abstract

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.

Published
2018

2. Genome-wide sequence analyses of ethnic populations across Russia

Author

Zhernakova, Daria V., Brukhin, Vladimir, Malov, Sergey, Oleksyk, Taras K., Koepfli, Klaus Peter, Zhuk, Anna, Dobrynin, Pavel, Kliver, Sergei, Cherkasov, Nikolay, Tamazian, Gaik, Rotkevich, Mikhail, Krasheninnikova, Ksenia, Evsyukov, Igor, Sidorov, Sviatoslav, Gorbunova, Anna, Chernyaeva, Ekaterina, Shevchenko, Andrey, Kolchanova, Sofia, Komissarov, Alexei, Simonov, Serguei, Antonik, Alexey, Logachev, Anton, Polev, Dmitrii E., Pavlova, Olga A., Glotov, Andrey S., Ulantsev, Vladimir, Noskova, Ekaterina, Davydova, Tatyana K., Sivtseva, Tatyana M., Limborska, Svetlana, Balanovsky, Oleg, Osakovsky, Vladimir, Novozhilov, Alexey, Puzyrev, Valery, and O'Brien, Stephen J.

Published
2020
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5. Tragopogon pratensis : Multiple introductions to North America, circumscription, and the formation of the allotetraploid T. miscellus

Author

Soltis, Douglas E., primary, Mavrodiev, Evgeny V., additional, Brukhin, Vladimir, additional, Roalson, Eric H., additional, Albach, Dirk C., additional, Godden, Grant T., additional, Alexeev, Yuri E., additional, Gitzendanner, Matthew A., additional, Freeman, Craig C., additional, Suárez‐Santiago, Víctor N., additional, and Soltis, Pamela S., additional

Published
2023
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8. First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species

Author

Ochkalova, Sofia, primary, Korchagin, Vitaly, additional, Vergun, Andrey, additional, Urin, Avel, additional, Zilov, Danil, additional, Ryakhovsky, Sergei, additional, Girnyk, Anastasiya, additional, Martirosyan, Irena, additional, Zhernakova, Daria V., additional, Arakelyan, Marine, additional, Danielyan, Felix, additional, Kliver, Sergei, additional, Brukhin, Vladimir, additional, Komissarov, Aleksey, additional, and Ryskov, Alexey, additional

Published
2022
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13. De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis

Author

Ryakhovsky, Sergei S., primary, Dikaya, Victoria A., additional, Korchagin, Vitaly I., additional, Vergun, Andrey A., additional, Danilov, Lavrentii G., additional, Ochkalova, Sofia D., additional, Girnyk, Anastasiya E., additional, Zhernakova, Daria V., additional, Arakelyan, Marine S., additional, Brukhin, Vladimir B., additional, Komissarov, Aleksey S., additional, and Ryskov, Alexey P., additional

Published
2021
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22. The Boechera Genus as a Resource for Apomixis Research

Author

Brukhin, Vladimir, Osadtchiy, Jaroslaw V, Florez-Rueda, Ana Marcela, Smetanin, Dmitry, Bakin, Evgeny, Nobre, Margarida Sofia, Grossniklaus, Ueli, Brukhin, Vladimir, Osadtchiy, Jaroslaw V, Florez-Rueda, Ana Marcela, Smetanin, Dmitry, Bakin, Evgeny, Nobre, Margarida Sofia, and Grossniklaus, Ueli

Abstract

he genera Boechera (A. Löve et D. Löve) and Arabidopsis, the latter containing the model plant Arabidopsis thaliana, belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera, such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.

Published
2019

23. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

Author

Kliver, Sergei, primary, Rayko, Mike, additional, Komissarov, Alexey, additional, Bakin, Evgeny, additional, Zhernakova, Daria, additional, Prasad, Kasavajhala V. S. K., additional, Rushworth, Catherine, additional, Baskar, R., additional, Smetanin, Dmitry, additional, Schmutz, Jeremy, additional, Rokhsar, Daniel S., additional, Mitchell-Olds, Thomas, additional, Grossniklaus, Ueli, additional, and Brukhin, Vladimir, additional

Published
2018
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25. Additional file 1 of Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, Shiping Liu, Gaik Tamazian, Zijun Xiong, Yurchenko, Andrey, Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Küntzel, Anne, Klaus-Peter Koepfli, Johnson, Warren, Kuderna, Lukas, GarcíA-Pérez, Raquel, Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Weilin Qiu, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras, Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Guojie Zhang, and O’Brien, Stephen

Abstract

Supplemental figures. Figure S1. Cheetah genome size estimation by 17-mers. Figure S2. Depth distribution of cheetah reads. Figure S3. GC content and average sequencing depth values. Figure S4. Depth distribution of re-sequencing reads. Figure S5. Distribution of syntenic blocks in genome windows. Figure S6. Ten largest cat-cheetah rearrangements. Figure S7. Size of homozygosity stretches in Felidae genomes. Figure S8. Ideograms of homozygosity regions. Figure S9. Comparison of cheetah and human MHC regions. Figure S10. Comparison of cheetah and dog MHC regions. Figure S11. Inferred historical population sizes by PSMC analysis. Figure S12. Bootstrap values for DaDi demographic models. Figure S13. Alignments of the AKAP4 gene. Figure S14. Evolutionary history of LDH gene families. Figure S15. Cumulative distribution of 36-mers. Figure S16. Copy-number distribution in control regions. Figure S17. Example of fixed duplications on scaffold606. (PDF 2027 kb)

Published
2015
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26. Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Kuentzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, Kuderna, Lukas F. K., Garcia-Perez, Raquel, de Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Qiu, Weilin, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras K., Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, O'Brien, Stephen J., Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Kuentzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, Kuderna, Lukas F. K., Garcia-Perez, Raquel, de Manuel, Marc, Godinez, Ricardo, Komissarov, Aleksey, Makunin, Alexey, Brukhin, Vladimir, Qiu, Weilin, Zhou, Long, Li, Fang, Yi, Jian, Driscoll, Carlos, Antunes, Agostinho, Oleksyk, Taras K., Eizirik, Eduardo, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, and O'Brien, Stephen J.

Published
2015

27. Genomic legacy of the African cheetah, Acinonyx jubatus

Author

Dobrynin, Pavel, primary, Liu, Shiping, additional, Tamazian, Gaik, additional, Xiong, Zijun, additional, Yurchenko, Andrey A., additional, Krasheninnikova, Ksenia, additional, Kliver, Sergey, additional, Schmidt-Küntzel, Anne, additional, Koepfli, Klaus-Peter, additional, Johnson, Warren, additional, Kuderna, Lukas F.K., additional, García-Pérez, Raquel, additional, Manuel, Marc de, additional, Godinez, Ricardo, additional, Komissarov, Aleksey, additional, Makunin, Alexey, additional, Brukhin, Vladimir, additional, Qiu, Weilin, additional, Zhou, Long, additional, Li, Fang, additional, Yi, Jian, additional, Driscoll, Carlos, additional, Antunes, Agostinho, additional, Oleksyk, Taras K., additional, Eizirik, Eduardo, additional, Perelman, Polina, additional, Roelke, Melody, additional, Wildt, David, additional, Diekhans, Mark, additional, Marques-Bonet, Tomas, additional, Marker, Laurie, additional, Bhak, Jong, additional, Wang, Jun, additional, Zhang, Guojie, additional, and O’Brien, Stephen J., additional

Published
2015
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29. Annotated features of domestic cat – Felis catus genome

Author

Tamazian, Gaik, primary, Simonov, Serguei, additional, Dobrynin, Pavel, additional, Makunin, Alexey, additional, Logachev, Anton, additional, Komissarov, Aleksey, additional, Shevchenko, Andrey, additional, Brukhin, Vladimir, additional, Cherkasov, Nikolay, additional, Svitin, Anton, additional, Koepfli, Klaus-Peter, additional, Pontius, Joan, additional, Driscoll, Carlos A, additional, Blackistone, Kevin, additional, Barr, Cristina, additional, Goldman, David, additional, Antunes, Agostinho, additional, Quilez, Javier, additional, Lorente-Galdos, Belen, additional, Alkan, Can, additional, Marques-Bonet, Tomas, additional, Menotti-Raymond, Marylin, additional, David, Victor A, additional, Narfström, Kristina, additional, and O’Brien, Stephen J, additional

Published
2014
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31. The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintainMEDEAparental imprinting

Author

Dumbliauskas, Eva, primary, Lechner, Esther, additional, Jaciubek, Miłosława, additional, Berr, Alexandre, additional, Pazhouhandeh, Maghsoud, additional, Alioua, Malek, additional, Cognat, Valerie, additional, Brukhin, Vladimir, additional, Koncz, Csaba, additional, Grossniklaus, Ueli, additional, Molinier, Jean, additional, and Genschik, Pascal, additional

Published
2011
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33. The Genome Russia project: closing the largest remaining omission on the world Genome map.

Author

Brukhin, Vladimir, O'Brien, Stephen J., and Oleksyk, Taras K.

Subjects
*HUMAN genetic variation, *GENE mapping, *NUCLEOTIDE sequencing
Abstract

We are witnessing the great era of genome exploration of the world, as genetic variation in people is being detailed across multiple varied world populations in an effort unprecedented since the first human genome sequence appeared in 2001. However, these efforts have yet to produce a comprehensive mapping of humankind, because important regions of modern human civilization remain unexplored. The Genome Russia Project promises to fill one of the largest gaps, the expansive regions across the Russian Federation, informing not just medical genomics of the territories, but also the migration settlements of historic and pre-historic Eurasian peoples. [ABSTRACT FROM AUTHOR]

Published
2015
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34. Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm, Norway spruce

Author

Filonova, Lada H., Bozhkov, Peter V., Brukhin, Vladimir B., Daniel, Geoffrey, Zhivotovsky, Boris, and Arnold, Sara von

Abstract

In the animal life cycle, the earliest manifestations of programmed cell death (PCD) can already be seen during embryogenesis. The aim of this work was to determine if PCD is also involved in the elimination of certain cells during plant embryogenesis. We used a model system of Norway spruce somatic embryogenesis, which represents a multistep developmental pathway with two broad phases. The first phase is represented by proliferating proembryogenic masses (PEMs). The second phase encompasses development of somatic embryos, which arise from PEMs and proceed through the same sequence of stages as described for their zygotic counterparts. Here we demonstrate two successive waves of PCD, which are implicated in the transition from PEMs to somatic embryos and in correct embryonic pattern formation, respectively. The first wave of PCD is responsible for the degradation of PEMs when they give rise to somatic embryos. We show that PCD in PEM cells and embryo formation are closely interlinked processes, both stimulated upon withdrawal or partial depletion of auxins and cytokinins. The second wave of PCD eliminates terminally differentiated embryo-suspensor cells during early embryogeny. During the dismantling phase of PCD, PEM and embryo-suspensor cells exhibit progressive autolysis, resulting in the formation of a large central vacuole. Autolytic degradation of the cytoplasm is accompanied by lobing and budding-like segmentation of the nucleus. Nuclear DNA undergoes fragmentation into both large fragments of about 50 kb and multiples of approximately 180 bp. The tonoplast rupture is delayed until lysis of the cytoplasm and organelles, including the nucleus, is almost complete. The protoplasm then disappears, leaving a cellular corpse represented by only the cell wall. This pathway of cell dismantling suggests overlapping of apoptotic and autophagic types of PCD during somatic embryogenesis in Norway spruce.

Published
2000
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35. Female gametophyte development and embryogenesis in Taxus baccata L.

Author

Brukhin, Vladimir B., Bozhkov, Peter V., Brukhin, Vladimir B., and Bozhkov, Peter V.

Abstract

Crassinucellate ovules are initiated in Taxus, directly from the shoot apex. The rudimentary pollen chamber is formed in the nucellus. A linear tetrad of megaspores with a functional chalazal megaspore is formed. A free-nuclear stage is charac-teristic at the beginning of megagametophyte development. Archegonia without ventral canal cell are solitary or in complexes. The embryo has a very long suspensor even after maturation. Two types of polyembryony have been revealed: i) embryogenic redifferentiation of suspensor cells and ii) cleavage of embryonic region in the early embryo. In the northern temperate climate of St. Petersburg one month delay in development of reproductive structures has been noted.

36. The Boechera Genus as a Resource for Apomixis Research

Author

Vladimir Brukhin, Jaroslaw V. Osadtchiy, Ana Marcela Florez-Rueda, Dmitry Smetanin, Evgeny Bakin, Margarida Sofia Nobre, Ueli Grossniklaus, University of Zurich, and Brukhin, Vladimir

Subjects
0106 biological sciences, 0301 basic medicine, Population, Asexual reproduction, Genomics, Review, Plant Science, lcsh:Plant culture, 580 Plants (Botany), Biology, 01 natural sciences, Genome, Boechera, 03 medical and health sciences, 10126 Department of Plant and Microbial Biology, Apomixis, pseudogamy, 1110 Plant Science, genomics, heterozygosity, lcsh:SB1-1110, 10211 Zurich-Basel Plant Science Center, education, diplospory, education.field_of_study, biology.organism_classification, 030104 developmental biology, Pseudogamy, Evolutionary biology, apomeiosis, genome assembly, apomixis, Ploidy, 010606 plant biology & botany
Abstract

The genera Boechera (A. Löve et D. Löve) and Arabidopsis, the latter containing the model plant Arabidopsis thaliana, belong to the same clade within the Brassicaceae family. Boechera is the only among the more than 370 genera in the Brassicaceae where apomixis is well documented. Apomixis refers to the asexual reproduction through seed, and a better understanding of the underlying mechanisms has great potential for applications in agriculture. The Boechera genus currently includes 110 species (of which 38 are reported to be triploid and thus apomictic), which are distributed mostly in the North America. The apomictic lineages of Boechera occur at both the diploid and triploid level and show signs of a hybridogenic origin, resulting in a modification of their chromosome structure, as reflected by alloploidy, aneuploidy, substitutions of homeologous chromosomes, and the presence of aberrant chromosomes. In this review, we discuss the advantages of the Boechera genus to study apomixis, consider its modes of reproduction as well as the inheritance and possible mechanisms controlling apomixis. We also consider population genetic aspects and a possible role of hybridization at the origin of apomixis in Boechera. The molecular tools available to study Boechera, such as transformation techniques, laser capture microdissection, analysis of transcriptomes etc. are also discussed. We survey available genome assemblies of Boechera spp. and point out the challenges to assemble the highly heterozygous genomes of apomictic species. Due to these challenges, we argue for the application of an alternative reference-free method for the comparative analysis of such genomes, provide an overview of genomic sequencing data in the genus Boechera suitable for such analysis, and provide examples of its application.

Published
2019
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37. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

Author

Vladimir Brukhin, Ramamurthy Baskar, Evgeny Bakin, K.V.S.K. Prasad, Daniel S. Rokhsar, Mike Rayko, Jeremy Schmutz, Alexey Komissarov, Thomas Mitchell-Olds, Ueli Grossniklaus, Dmitry Smetanin, Sergei Kliver, Catherine A. Rushworth, Daria V. Zhernakova, University of Zurich, and Brukhin, Vladimir

Subjects
0301 basic medicine, assembly, 2716 Genetics (clinical), lcsh:QH426-470, Sequence assembly, Locus (genetics), 580 Plants (Botany), Genome, Boechera, Brassicaceae, genome, annotation, apomixis, Article, 03 medical and health sciences, 10126 Department of Plant and Microbial Biology, 1311 Genetics, Apomixis, Genetics, 10211 Zurich-Basel Plant Science Center, Genome size, Gene, Genetics (clinical), Phylogenetic tree, biology, Human Genome, biology.organism_classification, plant_sciences, lcsh:Genetics, 030104 developmental biology
Abstract

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.

Published
2018
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